Research has been directed to understanding lipid and fatty acid (FA) biosynthetic pathways, and genetic engineering has been used to introduce these biosynthetic pathways into host organisms. For example, a variety of different hosts including plants, algae, fungi, stramenopiles and yeast are being investigated as means for commercial polyunsaturated fatty acid (PUFA) production. Genetic engineering has demonstrated that the natural abilities of some hosts, even those natively limited to linoleic acid (LA, 18:2 omega-6) or alpha-linolenic acid (ALA, 18:3 omega-3) fatty acid production, can be substantially altered to result in high-level production of various long-chain omega-3/omega-6 PUFAs.
Although the literature reports a number of recent examples whereby various portions of the omega-3/omega-6 PUFA biosynthetic pathway responsible for EPA production have been introduced into plants and non-oleaginous yeast, significant efforts have focused on the use of the oleaginous yeast, Yarrowia lipolytica (U.S. Pat. Nos. 7,238,482; 7,932,077; U.S. Pat. Appl. Publ. No. 2009-0093543-A1; U.S. Pat. Appl. Publ. No. 2010-0317072-A1). Oleaginous yeast are defined as those yeast that are naturally capable of oil synthesis and accumulation, wherein oil accumulation is at least 25% of the cellular dry weight, or those yeast genetically engineered such that they become capable of oil synthesis and accumulation, wherein oil accumulation is at least 25% of the cellular dry weight.
Still there remains considerable interest in increasing lipid accumulation in fungi. Expression of malic enzyme in the cytosol in Saccharomyces cerevisiae has been shown to increase NADPH production (2004, dos Santos et al., Metabol. Engineering 6:352-363). Given the role of NADPH as a reducing agent in fatty acid synthesis, malic enzyme has been investigated as a possible factor for altering lipid production. Zhang et al. (2007, Microbiology 153:2013-2025) have found that overexpression of malic enzyme in wild type Mucor circinelloides leads to a 2.5-fold increase in lipid accumulation. Consistent with this finding, studies have shown that malic enzyme expression in M. circinelloides and Mortierella alpina is correlated with lipid accumulation (1999, Wynn et al., Microbiology 145:1911-1917; 2002, Ratledge, Biochem. Soc. Trans. 30:1047-1050). Also, a mutant Aspergillus nidulans isolate lacking malic enzyme activity was shown to accumulate half as much lipid as produced by A. nidulans strains having malic enzyme (1997, Wynn et al., Microbiology 143:253-257).
However, studies in wild type Y. lipolytica suggest that malic enzyme may not play as large a role in lipid production. Beopoulos et al. (2011, Appl. Microbiol. Biotechnol. 90:1193-1206) briefly report that the overexpression of the mitochondrial form of malic enzyme did not affect lipid accumulation in Y. lipolytica. 
Notwithstanding the foregoing disclosures, surprisingly, it has been found that the lipid content of a transgenic Yarrowia species, comprising an engineered polyunsaturated fatty acid biosynthetic pathway and having a lipid content of at least about 35% by weight of the dry cell weight of the Yarrowia species, can be increased by overexpressing cytosolic malic enzyme.